ReviewDeubiquitinating enzymes—the importance of driving in reverse along the ubiquitin–proteasome pathway
Introduction
The discovery and characterization of the ubiquitin system has been one of the most exciting developments in biology in the past two decades. During this period, our understanding of the covalent linking of ubiquitin via an isopeptide linkage to the ε-amino group of lysine residues on target proteins has evolved from that of an unusual post-translational modification of uncertain importance to one in which this modification is now recognized to control the steady-state levels of numerous key regulatory molecules in the cell and/or influence their localization and function. As all of these effects are related to the covalent linking of ubiquitin to proteins, much attention has been paid to characterizing the enzymes responsible for adding this moiety to proteins. However, analogous to the protein phosphorylation system where phosphatases play important regulatory roles, deubiquitinating enzymes probably play similarly important regulatory roles. In addition, ubiquitin has the unique feature of being encoded in the genome as a fusion protein either to itself or to a ribosomal subunit and so some deubiquitinating enzymes have the function of cleaving these linear ubiquitin fusions precisely into the monomeric proteins. Although deubiquitinating enzymes have been recognized for some time, they are less well characterized compared to those involved in ubiquitination. In this review, I will summarize basic information about the major families of deubiquitinating enzymes, emphasize recent advances and illustrate some of the questions that remain to be answered.
Section snippets
Structure and mechanism
Deubiquitinating enzymes can be grouped on the basis of sequence homology into two well defined classes—ubiquitin carboxy-terminal hydrolases (UCH), and ubiquitin processing proteases (UBPs), also referred to as ubiquitin specific proteases (USPs) (Fig. 1). Although sequence comparisons reveal two clearly distinct classes, current data do not permit assignment of equally distinct profiles of functions to each class. However, this lack of distinctiveness in function is not due to a recent
Processing of ubiquitin gene products
As the overall pathway of the ubiquitin system was deciphered, a number of sites at which deubiquitinating enzymes would act became evident. Many of these activities have indeed been confirmed to be present in various deubiquitinating enzymes following analysis in vitro or in vivo in Escherichia coli using model substrates. Ubiquitin is encoded in the genome as fusion proteins with either additional copies of ubiquitin arranged in tandem (Finley, Ozkaynak, & Varshavsky, 1987) or as a fusion
Regulation
Deubiquitinating enzymes manifest the various types of regulation generally found in enzymes. There is extensive evidence of transcriptional regulation. Some are expressed in tissue restricted (Liu et al., 1999, Wilkinson et al., 1989), developmentally regulated (al-Katib, Mohammad, Maki, & Smith, 1995; Lin et al., 2000), hormonally regulated manners (Zhu et al., 1997; Zhu, Carroll, Papa, Hochstrasser, & D’Andrea, 1996) or upon environmental stimulation (Hegde et al., 1997). Alternative
Clinical relevance
The implication of the ubiquitin system in a broad array of cellular functions indicates that abnormal function of the pathway will be a cause of numerous diseases. As enzymes involved in conjugation have become extensively characterized, this has been confirmed. Although examples of deubiquitinating enzymes causing disease are fewer, this will undoubtedly change as their characterization becomes more complete.
The importance of the ubiquitin system in regulating cell cycle would predict that
Future directions
At a molecular level, the lack of information on the three dimensional structure of the UBP/USP family of enzymes remains a challenge and is probably due to the apparent limited solubility of many of these enzymes. At the level of biochemical function, the precise reactions and enzymes involved in recycling ubiquitin remain incompletely described as reflected in the tentativeness of the proposed model (Fig. 4). Within the proteasome, the exact chemical reactions catalyzed by each of the
Acknowledgements
The author is a recipient of a Chercheur Boursier award from the Fonds de la Recherche en Santé du Québec. Research in the author’s laboratory is supported by grants from the Canadian Institutes of Health Research.
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